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Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing


Key message

A novel R gene was mapped to a locus on chromosome 11 from 30.42 to 30.85 Mb, which was proven to be efficient in the improvement of rice blast resistance.


Rice blast is a devastating fungal disease worldwide. The use of blast resistance (R) genes is the most important approach to control the disease in rice breeding. In the present study, we finely mapped a novel resistance gene Pi65(t), conferring a broad-spectrum resistance to the fungus Magnaporthe oryzae, using bulked segregant analysis in combination with next-generation sequencing technology. Segregation in a doubled haploid (DH) population and a BC1F2 population suggested that resistance to blast in Gangyu129 was likely conferred by a single dominant gene, designated Pi65(t); it was located on chromosome 11 from 30.20 to 31.20 Mb using next-generation sequencing. After screening recombinants with newly developed molecular markers, the region was narrowed down to 0.43 Mb, flanked by SNP-2 and SNP-8 at the physical location from 30.42 to 30.85 Mb based on the Nipponbare reference database in build 5. Using the software QTL IciMapping, Pi65(t) was further mapped to a locus between InDel-1 and SNP-4 with genetic distances of 0.11 and 0.98 cM, respectively. Within this region, 4 predicted R genes were found with nucleotide binding site and leucine-rich repeat (NBS-LRR) domains. We developed molecular markers to genotype 305 DH lines and found that InDel-1 was closely linked with Pi65(t). Using InDel-1, a new rice variety Chuangxin1 containing Pi65(t) was developed, and it is highly resistant to rice blast and produces a high yield in Liaoning province of China. This indicated that Pi65(t) could play a key role in the improvement of rice blast resistance.

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This work was supported by the National Natural Science Foundation of China (Grant No.31571993 and 31301636), and Natural science foundation of Liaoning Province in China (2014027027).

Author information

Correspondence to Wenjing Zheng or Xiaochun Lu.

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Conflict of interest

The authors declare no conflicts of interest in regard to this manuscript.

Ethical standards

We declare that these experiments comply with the ethical standards in China, where they were performed.

Additional information

W. Zheng and Y. Wang contributed equally to this work.

Communicated by M. Thomson.

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Zheng, W., Wang, Y., Wang, L. et al. Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing. Theor Appl Genet 129, 1035–1044 (2016).

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  • Doubled Haploid
  • Rice Variety
  • Doubled Haploid Line
  • Rice Blast
  • Doubled Haploid Population